How long are you there?
My favorite part of Philly is the Old City. Wander around there. Check out Independence Hall and other historical sites.
If you've got kids there's a great place called the Franklin Institute, which is a very interactive science museum.
Philly's art museum is very cool. You've got the obvious front step made famous in 'Rocky,' but the museum itself is great.
I grew up right across the river, but have never been to the Mutter Museum. It's high on my list of things to do during one of my trips to the East Coast, which I don't get to make as often as I'd like.
Definitely go to South Street and wander around, although it's not as cool as it used to be. You'll find Jim's Steaks down there. It's better than Pat's or Geno's.
Check out Penn's Landing, especially if there's any music going on when you're there. There used to be a great bar down that way called the Dicken's Inn.
Depending on how much time you have, you can drive out to Valley Forge.
Going to NJ is all about the shore. Hit AC and Margate, then travel over the Longport bridge to Somer's Point to get some top-gun wings at Charlie's. Then check out OC, get some pizza at Mack and Manco's.
If you've got time, drive down to Cape May. Beautiful town, and have dinner at the Lobster House.

I agree with Buck on Old City and the Franklin Institute. The FI currently has a very popular King Tut exhibit, which might require advance tickets. I've been wanting to check it out. The National Constitution Center is also supposed to be cool.

I think Dickens Inn is still there, but I haven't been in about 15 years.

How long will you be there and what kinds of things do you want to do?

BTW, I'm FIRMLY in the Pat's camp, but would also recommend Tony Luke's for a roast pork sandwich.